There are three major mucosal systems in the vertebrate body, the oral-gastrointestinal, the respiratory and the genitourinary systems. The mucosal systems provide a first line of protection against ingested and inhaled infectious agents. The mucus layer covering the mucosal epithelium acts as a physical and biochemical barrier. A tightly interlaced cell-to-cell network of epithelial cells and intraepithelial lymphocytes provides further non-specific protection against microorganisms. The organism also defends against invading microbes through non-specific (for example phagocytes) and specific (for example humoral and secretory antibodies and cell-mediated immunity) actions of the immune system. Lymphoid tissues such as the Peyer's patches in the digestive tract and nasopharynx-associated lymphoid tissue in the respiratory tract have been shown to be important inductive sites for the initiation of the acquired phase of antigen-specific immune responses that help protect the mucosa. Moreover, mucosal compartments, such as the respiratory, genitourinary and gastrointestinal tracts, contain a rich and complex microbial flora or microbiota, which include pathogens, symbionts, and commensals. Some components of the mucosal microbiota can serve as biological barriers by competing with pathogenic bacteria for food and space and, in some cases, by changing the conditions in their environment, such as pH or available iron. The mucosal microbiota may be affected by a number of factors. Immune responses against components of a mucosal compartment microbial flora may lead to changes in the microbial flora. For example, immunization against respiratory pathogens such as H influenzae type B or S pneumoniae lead to elimination of those organisms from the upper respiratory flora. Therefore, induction of an immune response against a particular component of a mucosal compartment microbial flora can lead to substantial decreases in the relative abundance of that component.